SABA (secondary structure assignment program based on only alpha carbons): A novel pseudo center geometrical criterion for accurate assignment of protein secondary structures

Abstract

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-de-termined coordinates. Secondary structure assignment algorithms using limited Cα information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous Cαs. SABA is capable of identifying α-helices, 310-heli-ces, and β-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to Cα-only structures, algorithms using limited Cα information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.